MolNFT v1 · #63049 · protein
Crystal structure of kgpdc from streptococcus mutans in complex with D-R5P
3EXS · Rmpd (hexulose-6-phosphate synthase): “Crystal structure of kgpdc from streptococcus mutans in complex with D-R5P”. X-ray diffraction, 1 ligand (5RP), 8 pockets (best druggability 0.74). MolNFT v1 #63049 on GenesisL1: 3D structure…
- PDB
- 3EXS
- Type
- protein
- Length
- 845 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rmpd (hexulose-6-phosphate synthase)
- EC
- 4.1.1.85
- UniProt
- Q93DA8
- Ligands
- 5RP
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Rmpd (hexulose-6-phosphate synthase) (EC 4.1.1.85) | protein | 208 | 48% helix, 20% strand | Q93DA8 |
| B | Rmpd (hexulose-6-phosphate synthase) (EC 4.1.1.85) | protein | 211 | 47% helix, 20% strand | Q93DA8 |
| D | Rmpd (hexulose-6-phosphate synthase) (EC 4.1.1.85) | protein | 218 | 49% helix, 20% strand | Q93DA8 |
Ligands and binding sites
- 5RP · Ribulose-5-phosphate · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.74 | 0.94 | 36 | 5RP |
| 2 | 253 | 0.65 | 0.82 | 40 | 5RP |
| 3 | 283 | 0.57 | 0.77 | 43 | empty |
| 4 | 234 | 0.57 | 0.79 | 34 | empty |
| 5 | 222 | 0.56 | 0.79 | 34 | empty |
Interfaces
2 interfaces between chains.
- B–D · 1257 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1135 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3EXS · Crystal structure of KGPDC from Streptococcus mutans in complex with D-R5P · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q93DA8
- Elsewhere: RCSB PDB 3EXS · PDBe 3EXS · UniProt Q93DA8
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